[gmx-developers] Gromacs-2016: Win64 quasi-portable

Mon Oct 3 00:49:14 CEST 2016

On 10/2/16 6:30 PM, Boris Timofeev wrote:
> Dear Justin!
>
> Sorry, HISE, not HIZE.
>
> "Will use HISE for residue 15" - output from
> ..\src\gromacs\gmxpreprocess\hizzie.cpp, line 342
>
> There is copy of cmdline output.
>
> Microsoft Windows [Version 6.1.7601]
> (c) Корпорация Майкрософт (Microsoft Corp.), 2009. Все права защищены.
>
> C:\Users\BorisTimofeev>cd ..
>
> C:\Users>cd ..
>
> C:\>cd gromacs-2016
>
> C:\gromacs-2016>cd mysamples
>
> C:\gromacs-2016\mysamples>gmx pdb2gmx -f 1AKI.pdb -o 1AKI_processed.gro -water spce
> :-) GROMACS - gmx pdb2gmx, 2016 (-:
>
> GROMACS is written by:
> Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
> Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof
> Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis
> Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
> Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund
> Teemu Murtola Szilard Pall Sander Pronk Roland Schulz
> Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman
> Teemu Virolainen Christian Wennberg Maarten Wolf
> and the project leaders:
> Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
>
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2015, The GROMACS development team at
> Uppsala University, Stockholm University and
> the Royal Institute of Technology, Sweden.
> check out http://www.gromacs.org for more information.
>
> GROMACS is free software; you can redistribute it and/or modify it
> under the terms of the GNU Lesser General Public License
> as published by the Free Software Foundation; either version 2.1
> of the License, or (at your option) any later version.
>
> GROMACS: gmx pdb2gmx, version 2016
> Executable: C:\gromacs-2016\build\bin\Release\gmx.exe
> Data prefix: C:\gromacs-2016 (source tree)
> Working dir: C:\gromacs-2016\mysamples
> Command line:
> gmx pdb2gmx -f 1AKI.pdb -o 1AKI_processed.gro -water spce
>
>
> Select the Force Field:
> From 'C:/gromacs-2016/share/top':
> 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012,
> 2003)
> 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
> 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29,
> 461-469, 1996)
> 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074,
> 2000)
> 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)
> 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78,
> 1950-58, 2010)
> 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
> 8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
> 9: GROMOS96 43a1 force field
> 10: GROMOS96 43a2 force field (improved alkane dihedrals)
> 11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
> 12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
> 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
> 14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI:
> 10.1007/s00249-011-0700-9)
> 15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
> 15
>
> Using the Oplsaa force field in directory oplsaa.ff
>
> Opening force field file C:\gromacs-2016/share/top/oplsaa.ff/aminoacids.r2b
> Reading 1AKI.pdb...
> WARNING: all CONECT records are ignored
> Read 'LYSOZYME', 1079 atoms
> Analyzing pdb file
> Splitting chemical chains based on TER records or chain id changing.
> There are 1 chains and 1 blocks of water and 207 residues with 1079 atoms
>
> chain #res #atoms
> 1 'A' 129 1001
> 2 ' ' 78 78 (only water)
>
>
> WARNING: there were 0 atoms with zero occupancy and 74 atoms with
> occupancy unequal to one (out of 1079 atoms). Check your pdb file.
>
> Opening force field file C:\gromacs-2016/share/top/oplsaa.ff/atomtypes.atp
> Atomtype 814
> Reading residue database... (oplsaa)
> Opening force field file C:\gromacs-2016/share/top/oplsaa.ff/aminoacids.rtp
> Residue 52
> Sorting it all out...
> Opening force field file C:\gromacs-2016/share/top/oplsaa.ff/aminoacids.hdb
> Opening force field file C:\gromacs-2016/share/top/oplsaa.ff/aminoacids.n.tdb
> Opening force field file C:\gromacs-2016/share/top/oplsaa.ff/aminoacids.c.tdb
>
> Back Off! I just backed up topol.top to ./#topol.top.4#
> Processing chain 1 'A' (1001 atoms, 129 residues)
> Analysing hydrogen-bonding network for automated assignment of histidine
> protonation. 213 donors and 184 acceptors were found.
> There are 255 hydrogen bonds
> Will use HISE for residue 15
> Identified residue LYS1 as a starting terminus.
> Identified residue LEU129 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Special Atom Distance matrix:
> CYS6 MET12 HIS15 CYS30 CYS64 CYS76 CYS80
> SG48 SD87 NE2118 SG238 SG513 SG601 SG630
> MET12 SD87 1.166
> HIS15 NE2118 1.776 1.019
> CYS30 SG238 1.406 1.054 2.069
> CYS64 SG513 2.835 1.794 1.789 2.241
> CYS76 SG601 2.704 1.551 1.468 2.116 0.765
> CYS80 SG630 2.959 1.951 1.916 2.391 0.199 0.944
> CYS94 SG724 2.550 1.407 1.382 1.975 0.665 0.202 0.855
> MET105 SD799 1.827 0.911 1.683 0.888 1.849 1.461 2.036
> CYS115 SG889 1.576 1.084 2.078 0.200 2.111 1.989 2.262
> CYS127 SG981 0.197 1.072 1.721 1.313 2.799 2.622 2.934
> CYS94 MET105 CYS115
> SG724 SD799 SG889
> MET105 SD799 1.381
> CYS115 SG889 1.853 0.790
> CYS127 SG981 2.475 1.686 1.483
> Linking CYS-6 SG-48 and CYS-127 SG-981...
> Linking CYS-30 SG-238 and CYS-115 SG-889...
> Linking CYS-64 SG-513 and CYS-80 SG-630...
> Linking CYS-76 SG-601 and CYS-94 SG-724...
> Start terminus LYS-1: NH3+
> End terminus LEU-129: COO-
> Checking for duplicate atoms....
> Generating any missing hydrogen atoms and/or adding termini.
> Now there are 129 residues with 1960 atoms
> Making bonds...
> Number of bonds was 1984, now 1984
> Generating angles, dihedrals and pairs...
> Before cleaning: 5142 pairs
> Before cleaning: 5187 dihedrals
> Keeping all generated dihedrals
> Making cmap torsions...
> There are 5187 dihedrals, 426 impropers, 3547 angles
> 5106 pairs, 1984 bonds and 0 virtual sites
> Total mass 14313.193 a.m.u.
> Total charge 7.887 e
> Writing topology
>
> Back Off! I just backed up posre.itp to ./#posre.itp.3#
> Processing chain 2 (78 atoms, 78 residues)
> Problem with chain definition, or missing terminal residues.
> This chain does not appear to contain a recognized chain molecule.
> If this is incorrect, you can edit residuetypes.dat to modify the behavior.
> 8 out of 8 lines of specbond.dat converted successfully
> Checking for duplicate atoms....
> Generating any missing hydrogen atoms and/or adding termini.
> Now there are 78 residues with 234 atoms
> Making bonds...
> Number of bonds was 156, now 156
> Generating angles, dihedrals and pairs...
> Making cmap torsions...
> There are 0 dihedrals, 0 impropers, 78 angles
> 0 pairs, 156 bonds and 0 virtual sites
> Total mass 1405.201 a.m.u.
> Total charge 0.000 e
> Including chain 1 in system: 1960 atoms 129 residues
> Including chain 2 in system: 234 atoms 78 residues
> Now there are 2194 atoms and 207 residues
> Total mass in system 15718.394 a.m.u.
> Total charge in system 7.887 e
>

Yep, that's clearly a bug.  I see what happened and will upload a patch.

-Justin

> Writing coordinate file...
>
> Back Off! I just backed up 1AKI_processed.gro to ./#1AKI_processed.gro.2#
> --------- PLEASE NOTE ------------
> You have successfully generated a topology from: 1AKI.pdb.
> The Oplsaa force field and the spce water model are used.
> --------- ETON ESAELP ------------
>
> GROMACS reminds you: "If I Were You I Would Give Me a Break" (F. Black)
>
>
> From file topol.top:  qtot
>
> 227 opls_235 14 ARG C 74 0.5 12.011 ; qtot 4.5
> 228 opls_236 14 ARG O 74 -0.5 15.9994 ; qtot 4
> ; residue 15 HIS rtp HISE q -0.1
> 229 opls_238 15 HIS N 75 -0.5 14.0067 ; qtot 3.5
> 230 opls_241 15 HIS H 75 0.3 1.008 ; qtot 3.8
> 231 opls_224B 15 HIS CA 75 0.14 12.011 ; qtot 3.94
> 232 opls_140 15 HIS HA 75 0.06 1.008 ; qtot 4
> 233 opls_505 15 HIS CB 76 -0.005 12.011 ; qtot 3.995
> 234 opls_140 15 HIS HB1 76 0.06 1.008 ; qtot 4.055
> 235 opls_140 15 HIS HB2 76 0.06 1.008 ; qtot 4.115
> 236 opls_507 15 HIS CG 77 -0.015 12.011 ; qtot 4.1
> 237 opls_511 15 HIS ND1 77 -0.49 14.0067 ; qtot 3.61
> 238 opls_508 15 HIS CD2 78 0.015 12.011 ; qtot 3.625
> 239 opls_146 15 HIS HD2 78 0.115 1.008 ; qtot 3.74
> 240 opls_506 15 HIS CE1 79 0.182 12.011 ; qtot 3.922
> 241 opls_146 15 HIS HE1 79 0.115 1.008 ; qtot 4.037
> 242 opls_503 15 HIS NE2 80 -0.57 14.0067 ; qtot 3.467
> 243 opls_504 15 HIS HE2 80 0.42 1.008 ; qtot 3.887
> 244 opls_235 15 HIS C 81 0.5 12.011 ; qtot 4.387
> 245 opls_236 15 HIS O 81 -0.5 15.9994 ; qtot 3.887
> ; residue 16 GLY rtp GLY q 0.0
> 246 opls_238 16 GLY N 82 -0.5 14.0067 ; qtot 3.387
> 247 opls_241 16 GLY H 82 0.3 1.008 ; qtot 3.687
>
>
>
>
>
>
>
>     Понедельник, 3 октября 2016, 1:01 +03:00 от Justin Lemkul <jalemkul at vt.edu>:
>
>
>
>     On 10/2/16 5:42 PM, Boris Timofeev wrote:
>     >
>     > Good afternoon to all!
>     >
>     > I did a great job on compilation of the "portable" Gromacs-2016 version on the
>     > Win64 platform without cygwin with OpenCL support and AVX_256/AVX2_256
>     > expansions. The project is builded on VS-2015. By small changes in
>     CMakeLists, I
>     > managed to achieve that both the "embedded" tests, and regressiontests, are
>     > executed after assembly immediately from VS IDE. It was tested on Windows7/
>     > Windows10 with IntelCore i3, i5, i7 processors and video cards from Nvidia and
>     > AMD. So far it was not succeeded to win - against the video card from Intel -
>     > Intel OpenCL compiler preprocessor is left unfinished, does not recognize
>     > directive "-I" and have buggy concatention (##) implementation.
>     > It was necessary to realize a primitive preprocessor, became successful, but
>     > all the same calculations (tests and regressiontests) are wrong as it was
>     > already metioned here (https://bugs.freedesktop.org/show_bug.cgi?
>     > id=94265#add_comment).
>     >
>     > If it is interesting to community, I am ready to report about some necessary
>     > changes in progect and to provide the main CMake-file.
>     >
>     > There are several questions to developers.
>     >
>     > 1. The nbnxn_ocl_kernel_nvidia.clh, nbnxn_ocl_kernel_nowarp.clh and
>     > nbnxn_ocl_kernel_amd.clh files, if to compare their with kdiff, differ only in
>     > comments and lack of unroll pragma for Nvidia. Why not to unite them in one?
>     > Where the promised optimization?
>     >
>     > 2. Why in the Gromacs'a code so many paths to files are embedded up? To start
>     > tests without development environment on other computer it is necessary to
>     copy
>     > practically all project.
>     >
>     > 3. A question "on science". When performing an example of
>     >
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html,
>     > pdb2gmx for the aminoacid residue HIS ("HIZE-branch" on stdout ), unlike all
>     > others residue, gives a nonintegral charge 0.883, inexplicable with round-off
>     > errors.
>     > Whether there is no program mistake here?
>     >
>
>     I can't speak to points 1 and 2, but here: what is HIZE-branch? I've never
>     heard of that. Note, too, that if you're working with a single amino acid with
>     OPLS-AA, you can't rely on the default terminus selection. You need to choose
>     the zwitterion termini, otherwise the charges will be junk because OPLS-AA
>     makes
>     changes to CA depending on whether the residue is a zwitterion or in a
>     polypeptide.
>
>     -Justin
>
>     --
>     ==================================================
>
>     Justin A. Lemkul, Ph.D.
>     Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
>     Department of Pharmaceutical Sciences
>     School of Pharmacy
>     Health Sciences Facility II, Room 629
>     University of Maryland, Baltimore
>     20 Penn St.
>     Baltimore, MD 21201
>
>     jalemkul at outerbanks.umaryland.edu <mailto:jalemkul at outerbanks.umaryland.edu>
>     | (410) 706-7441
>     http://mackerell.umaryland.edu/~jalemkul
>
>     ==================================================
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================